The overarching goal of our CCHI application on “Vaccine and Infection Induced Immunity in the Young and Aged” is to address fundamental issues about innate and adaptive immunity in humans to infection and vaccination. Our proposal is focused around a large cohort of > 700 COVID-19 patients that we have been following for the past 3 years and now propose to follow for an additional 5 years during the course of this proposal. These patients were recruited at our two clinical research sites, Emory University (Atlanta, Georgia) and Fred Hutchinson Cancer Center (Seattle, Washington). Our combined cohort of > 700 patients consists of individuals who were first infected with SARS-CoV-2 and then received the mRNA Pfizer or Moderna vaccine, and some individuals who got the vaccine first and were then infected. Several of these individuals then had booster shots and some also had breakthrough infections. During this 3 year period of multiple antigen encounters we have collected on average between 5-10 blood samples from each patient. We now propose to collect 3-4 samples/year from each patient for the next 5 years. The longitudinal assessment of innate, humoral and cellular immunity in this large cohort over an 8 year period with 20-30 time points for each person will provide an extraordinary and unprecedented look at the durability and evolution adaptive and innate immunity following infection and vaccination. These studies will not only provide insight into the underlying mechanisms of innate immunity and long-term immune memory but will also inform how we develop optimal vaccination strategies against SARS-CoV-2 and other emerging viral infections. We have assembled a group of outstanding investigators from five institutions with highly complementary expertise and organized our renewal application along the following Projects and Cores: Project 1: Immune Memory: Drs. Rafi Ahmed and Julie McElrath; Project 2: Innate Immunity: Drs. Bali Pulendran and Donna Farber; Core A: Administrative: Dr. Rafi Ahmed; Core B: Genomics Core: Drs. Steve Bosinger and William Greenleaf; Core C: Clinical and Biostatistics: Drs. Sri Edupuganti, Julie McElrath, Max Lau, and Veronika Zarnitsyna. The overall broad Aims of our CCHI program are as follows: Aim 1: Longitudinal analysis of T and B cell responses to SARS-CoV-2. Aim 2: Innate Immunity with focus on functional and epigenetics changes in myeloid cells.
Our comprehensive proposed studies using our large COVID-19 cohort will assess innate, and humoral and cellular immunity over an 8-year period. This provides an extraordinary and unprecedented look at the durability and evolution of human T and B cell memory after vaccination and infection. This will provide insight into the underlying mechanisms of long-term immune memory and also inform how we develop optimal vaccination strategies against emerging viral infections.
Visit our website at http://vaccines.emory.edu/
Our U19 Center consists of three Cores and two Projects:
CORE A: ADMINISTRATIVE CORE
AHMED, RAFI, Core Lead
The major objectives of the Administrative Core of the Cooperative Center on Human Immunology at the Emory Vaccine Center (CCHI-EVC) are to institute streamlined processes facilitating productive interactions among the investigators of the renewal grant application entitled “Vaccine and Infection Induced Immunity in the Young and Aged”. To achieve these objectives and to ensure a seamless operation of the Core, we will establish an Administrative Core Committee (ACC) for carrying out the following activities/functions at the CCHI- EVC: 1) Provide the infrastructure for the overall management and co-ordination at the Center. 2) Facilitate and promote communication and interaction among the PIs/investigators (Research Projects 1-3 and Cores B and C) by conducting regular progress Zoom/face-to-face meetings, annual meetings, as well as seminars/symposia on human immunology. 3) Provide fiscal/scientific/core oversight, review and consolidate yearly progress reports sent to the NIH. 4) Protect intellectual property rights of CCHI-EVC investigators and to execute material transfer agreements. 5) Resolve all or any potential conflicts that might arise within and outside of CCHI- EVC by implementing recommendations of the Conflicts Resolution Group. 6) Devise a plan for data management/sharing among investigators in and out of CCHI-EVC and to deposit data to ImmPort, as per the mandates of NIH policy Thus, the Administrative Core is organized to foster a high degree of synergy and productive interaction among investigators for achieving success in the overall objectives of CCHI-EVC.
CORE B: GENOMICS CORE
BOSINGER, STEVEN EDWARD, Core Lead
Single-cell genomic technology has rapidly transformed modern immunology. In relatively few short years, single-cell RNA sequencing has become near ubiquitous, primarily due to the availability of robust commercial platforms. The ability to combine multiple forms of information simultaneously (i.e. multi-modal readouts) has proven to be of significant utility, particularly for dissecting the diversity of the adaptive immune system. Single- cell methodology is now capable of acquiring information on multiple modalities simultaneously: surface receptor levels, paired immune receptor (BCR/TCR) clonotype identity, chromatin accessibility and tissue localization, and other parameters can now be measured alongside the transcriptome in relatively routine technology. The goal of Core B is to support the activities of Projects 1-3 by applying tailored advances in single-cell biology that are not commercially available. In Aim 1, we will apply single-cell DNA bar-coding technology capable of assessing B cell specificity to SARS-CoV Spike protein epitopes from major variants. The application of this technology, capable of resolution of epitope specific responses would address several needs in SARS-CoV-2 research: (i) it accelerates the discovery of potential broadly neutralizing antibodies against SARS-CoV-2; (ii) it would afford comprehensive profiling of S protein variant specificity, (iii) it would provide a rich set of immunoglobulin sequence data to measure antibody evolution in distinct epitope specificities. In Aim 2, we will develop panels of DNA-linked antibodies to assay the protein abundance of master regulator transcription factors associated with the innate and adaptive immune system (NEAT-Seq). The ability to profile transcription factors provides the necessary granularity to dissect precise immune cell phenotypes and ontogeny, which will be critical in understanding the impact of senescence of SARS-CoV-2 specific cells in Project 2. Finally, in Aim 3, we will conduct spatial transcriptomics in support of Project 2, to profile the localization of macrophages in cadaver and NHP tissues from SARS-CoV-2 infected and vaccinated individuals. The activities of Core B leverage prior progress and parallel technology development by the MPIs. In the prior funding period, we developed novel methodology to obtain paired clonotype identity and transcriptome data in antigen-specific B cells, including development, validation and benchmarking of a novel bioinformatics algorithm capable of accurately reconstructing paired immunoglobulin gene sequences in vaccine-elicited B cells. Here, we extend our prior work to incorporate additional information: antigen specificity for SARS-CoV-2 epitopes. Additionally, in the prior period, we developed and NEAT-seq technology, a method for assaying the abundance of key transcription factors simultaneously with chromatin accessibility and the transcriptome. At the conclusion of the activities of Core B, we will have applied novel, tailored technology to advance our understanding of variant-specific humoral immunity, and the “in tissue” regional specialization of the innate response after SARS-CoV-2 vaccination. Collectively, these activities will enhance the insight gained from the unique samples available to this consortium.
CORE C: CLINICAL AND BIOSTATISTIC CORE
EDUPUGANTI, SRILATHA, Core Lead
To support the research goals of our CCHI, the Clinical and Biostatistical Core proposes to continue long-term follow up of our established COVID-19 cohort of 747 patients over the next 5-year grant cycle. The unique features of COVID-19 immunity can be explored in this cohort, which presents an incredible opportunity to advance mechanistic insight into the induction of innate and adaptive immunity to a novel, highly transmissible pathogen that poses ongoing threats to human health. Knowledge gained from these immunological studies can inform approaches to control future emerging human coronaviruses that could become major public health concerns. The Specific Aims of the Clinical Core are: Aim 1. Provide the clinical infrastructure and expertise for conducting human research to improve mechanistic understanding of immunity following vaccination and infection among different age groups. Aim 2. Define immune memory in study participants enrolled in our COVID-19 longitudinal cohort who recover or experience Long COVID. Aim 3. Provide statistical, modeling, and data management expertise that ensures the success of the CCHI scientific agenda.
PROJECT 1: IMMUNE MEMORY
AHMED, RAFI, Project Lead
Our long-term goal is to understand the cellular and molecular basis of immunological memory in humans. We will address this important question in Project 1 by doing a detailed analysis of both humoral and cellular immunity in a longitudinal cohort of over > 700 COVID-19 patients that we have been following for the past three years and will now follow for another five years. These patients were recruited at our two clinical sites located in Atlanta (Emory University) and Seattle (Fred Hutchinson Cancer Center). This combined cohort consists of individuals who were first infected with SARS-CoV-2 and then got the Pfizer or Moderna mRNA vaccine, and some individuals who received the vaccine first and then got infected. Many of these individuals have then gotten booster shots with the vaccine and several of them have also had additional breakthrough infections. During this three-year period of multiple antigen encounters of various combinations of infection and vaccination, we have collected between 5-10 longitudinal blood samples from each patient. We now propose to follow these patients for another five years and will collect 3-4 samples per year from each patient. Thus, we will have 20-30 longitudinal blood samples from each patient over an 8-year period. In addition, in the next five years we will also collect bone marrow aspirates and mucosal samples from a subset of these individuals. The Specific Aims of Project 1 are as follows: Aim 1: To determine the magnitude and durability of humoral and cellular immunity in the entire cohort of > 700 COVID-19 patients over a period of 8 years. Aim 2: To examine the evolution of memory B cell responses and determine the longevity of bone marrow plasma cells. Aim 3. To track differentiation of T cells over time and define the transcriptional and epigenetic signatures of virus specific memory CD8 and CD4 T cells.
PROJECT 2: INNATE IMMUNITY
PULENDRAN, BALI, Project Lead
Immunological memory is a fundamental feature of the adaptive immune system. However emerging evidence demonstrates that the innate immune system can also display a form of adaptive, memory-like behavior, a phenomenon termed “trained immunity.” Recently using single cell ATAC-seq we demonstrated that immunization of humans with the AS03-adjuvanted H5N1 pandemic influenza vaccine stimulates persistent epigenomic imprints in blood myeloid cells, that results in a heightened resistance to infection with heterologous viruses Zika and Dengue viruses, and reduced chromatin accessibility of loci targeted by the AP-1 transcription factors leading to reduced capacity to produce pro-inflammatory cytokines. These observations raise several key questions: 1) Do SARS-CoV-2 infection and vaccination stimulate functionally distinct long-term epigenetic innate reprogramming? 2) Is epigenetic imprinting of innate immunity “tunable,” by sequential infections or vaccinations? 3) What is the impact of SARS-CoV-2 vaccination or infection on epigenetic imprinting of innate immunity in tissues? 4) What are the mechanisms of innate memory induced by vaccination and their effects on protection against heterologous pathogens? These questions will be addressed in the following specific aims: Aim 1. Perform a longitudinal analysis of the evolution of the innate response following sequential rounds of SARS-CoV-2 infection or vaccination. We will perform a longitudinal analysis of the single cell transcriptional and epigenetic landscape of the innate immune system using banked PBMCs collected before, during and after infection from a COVID-19 cohort of healthcare workers and followed longitudinally from the beginning of the pandemic, through every infection and vaccination. Aim 2. Define the transcriptional and epigenetic landscape and function of myeloid cells in tissues. Most studies have only examined epigenetic imprinting of innate immunity in the blood, and the effects in tissues remain unclear. In sub-aim 2a we will assess the transcriptional and epigenomic landscape of myeloid-lineage cells in human mucosal and lymphoid tissues obtained from organ donors. In sub-aim 2b, we will use banked samples from completed studies in nonhuman primates to assess the transcriptional and epigenomic landscape of innate immune cells in various tissues and blood following SARS-CoV-2 infection or vaccination. Aim 3: To assess the mechanisms of innate memory induced by vaccination and their effects on protection against heterologous pathogens. In this aim we will use mice to explore the mechanisms underlying innate memory to vaccination, and its functional consequences on protection against heterologous infections.
